This really isn't based on anything. I have just always assumed it was because the virus was so potant down there. everyone else picked it up from charlie or his family coughing on them, and then those people coughing on the next and so on. so they only got a bit. but the people in the base, they had it striaght in the air. thousands of little flu buggers attacking them at once.
But like I said, that is always what I assumed. after the virus spread out people had build ups to it or whatever, and the virus had to work harder at mutating to kill them.